6BSH

Structure of HIV-1 RT complexed with RNA/DNA hybrid in the RNA hydrolysis mode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid.

Tian, L.Kim, M.S.Li, H.Wang, J.Yang, W.

(2018) Proc Natl Acad Sci U S A 115: 507-512

  • DOI: 10.1073/pnas.1719746115
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • HIV-1 reverse transcriptase (RT) contains both DNA polymerase and RNase H activities to convert the viral genomic RNA to dsDNA in infected host cells. Here we report the 2.65-Å resolution structure of HIV-1 RT engaging in cleaving RNA in an RNA/DNA h ...

    HIV-1 reverse transcriptase (RT) contains both DNA polymerase and RNase H activities to convert the viral genomic RNA to dsDNA in infected host cells. Here we report the 2.65-Å resolution structure of HIV-1 RT engaging in cleaving RNA in an RNA/DNA hybrid. A preferred substrate sequence is absolutely required to enable the RNA/DNA hybrid to adopt the distorted conformation needed to interact properly with the RNase H active site in RT. Substituting two nucleotides 4 bp upstream from the cleavage site results in scissile-phosphate displacement by 4 Å. We also have determined the structure of HIV-1 RT complexed with an RNase H-resistant polypurine tract sequence, which adopts a rigid structure and is accommodated outside of the nuclease active site. Based on this newly gained structural information and a virtual drug screen, we have identified an inhibitor specific for the viral RNase H but not for its cellular homologs.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; wei.yang@nih.gov.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REVERSE TRANSCRIPTASE P66 SUBUNIT
A
558Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
EC: 2.7.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REVERSE TRANSCRIPTASE P51 SUBUNIT
B
441Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for A0A076Q3N8 (Human immunodeficiency virus 1)
Go to UniProtKB:  A0A076Q3N8
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*AP*TP*GP*CP*CP*AP*CP*TP*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3')D23Homo sapiens

Find similar proteins by: Sequence   |  Structure

Entity ID: 4
MoleculeChainsLengthOrganism
RNA (25-MER)R25Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EFZ
Query on EFZ

Download CCD File 
A
(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
C14 H9 Cl F3 N O2
XPOQHMRABVBWPR-ZDUSSCGKSA-N
 Ligand Interaction
TAM
Query on TAM

Download CCD File 
R
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.792α = 90
b = 161.792β = 90
c = 128.773γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references